The NCBI BLAST AMI will be useful to a variety of users. The requirements for using it and how easy it will be to set up will depend on the user’s workflow and the level of expertise with setting up computing resources on a cloud service provider.

For those without a background in computers, having familiarity with cloud services is helpful, but not mandatory, as the AWS Marketplace provides a 1-Click-Launch option and documentation on how to start/stop your instances. If you run into any difficulty, please feel free to email us at so we can help you!

A typical scenario would be to have one user in a group/team to register at a cloud provider, configure the instance, and handle payment for the running instance(s). Other members of the group/team can then use the instance through the Common URL API or webpage without their own cloud provider account. The Common URL API interface is ideal for users familiar with the BLAST URL API at the NCBI. Currently, the BLAST server image runs searches on only one instance. Many simultaneous users, could overload a single instance, to avoid this monitor your instance.

Please see the table below for specific examples:

Task/workflow 1-click-start Knowledge of ssh/scp/networking Optimal data center region Programmatic access via Common URL API
BLAST against protein nr, swissprot,
refseq_protein, pdbaa, or
nucleotide nt, pdbnt, refseq_rna via web interface
Yes (1) Limited (4) us-east-1 (N. Virginia) Not applicable
BLAST your own/propietary sequence data (2,3) Limited options Required (4) Closest to where your data is stored Optional
Third party application developers to run BLAST (3) Limited options Required (4) Depends on user’s workflow (see two rows above) Likely required
Foot notes
  1. The 1-Click-Launch option is configured by default to start a m4.10xlarge instance (40 vCPUs, 160 GB RAM, EBS volumes, $2/hr), which is large enough (as of 06/08/2018) to run searches against the nr and nt BLAST databases and store the results in the instance’s local disk.
  2. For those users with proprietary sequence data, you can convert that sequence data into BLAST databases and upload the resulting BLAST databases to a running instance.
  3. Please be sure to choose an appropriately sized instance for your workload.
  4. Please see setting up remote access.